Atomistic modelling of entropy driven phase transitions between different crystal modifications in polymers: the case of poly(3-alkylthiophenes).

Polymorphism and related solid-state phase transitions affect the structure and morphology and hence the properties of materials, but they are not-so-well understood. Atomistic computational methods can provide molecular-level insights, but they have rarely proven successful for transitions between polymorphic forms of crystalline polymers. In this work, we report atomistic molecular dynamics (MD) simulations of poly(3-alkylthiophenes) (P3ATs), widely used organic semiconductors to explore the experimentally observed, entropy-driven transition from form II to more common form I type polymorphs, or, more precisely, to form I mesophases. The transition is followed continuously, also considering X-ray diffraction evidence, for poly(3-hexylthiophene) (P3HT) and poly(3-butylthiophene) (P3BT), evidencing three main steps: (i) loss of side chain interdigitation, (ii) partial disruption of the original stacking order and (iii) reorganization of polymer chains into new, tighter, main-chain stacks and new layers with characteristic form I periodicities, substantially larger than those in the original form II. The described approach, likely applicable to other important transitions in polymers, provides previously inaccessible insight into the structural organization and disorder features of form I structures of P3ATs, not only in their development from form II structures but also from melts or solutions.

Nucleophilicity and electrophilicity of the C(sp3)-H bond: methane and ethane binary complexes with iodine.

The occurrence of stable van der Waals complexes of small saturated hydrocarbons with molecular iodine is assessed in order to investigate the ability of sp3-hybridized carbon atoms to act as either electron donors or electron acceptors depending on the ligand orientation. Systematic ab initio potential energy surface exploration of methane-I2 and ethane-I2 model dimers was followed by thorough characterization. Despite modest evidence of whole-adduct polarization, the resulting interactions feature a dominant dispersive character. The noncovalent interaction descriptors employed comprise NBO, AIM, NCI, and source function analyses. The relevance of bonding C-H orbitals in donor-acceptor interactions involving saturated hydrocarbons is highlighted. The results here presented corroborate existing literature regarding the electrophilicity of the aliphatic C-H group, and also indicate that the nucleophilic character of C(sp3) shares a dependence on electron withdrawing/donating substituents similar to that extensively documented for σ-holes. Indeed, the sole difference between the two, aside from the nucleophilicity/electrophilicity switch, seems to lie in their directionality. Nucleophilic sites on C(sp3) are not limited to the outermost region of C along a covalent bond axis, but can also engage electrophiles via the bifurcation plane of a CH2 unit. Since valence electrons on these carbon atoms are engaged in covalent bonds, they can only interact with polarizing ligands via the electron density accumulation/depletion in the four corresponding σ orbitals. These, however, do not seem to interact individually with the accompanying electrophile. Source function and NCI results suggest instead that nucleophilic carbon centres participate in the noncovalent bond themselves by drawing electron density from their shared electron pairs.

Pyrrolidinium-based ionic liquids doped with lithium salts: how does Li(+) coordination affect its diffusivity?

We present the characterization of LiX-doped room-temperature ionic liquids (ILs) based on the N-butyl-N-methyl pyrrolidinium (PYR14) cation with two fluorinated anions: (trifluoromethanesulfonyl)-(nonafluorobutanesulfonyl)imide (X═IM14) and bis(pentafluoroethanesulfonyl)imide (X═BETI). The new data are also compared with previous results on PYR14TFSI (bis(trifluoromethanesulfonyl)imide). Their local organization has been investigated via NMR nuclear Overhauser effect (NOE) experiments for {(1)H-(19)F} and {(1)H-(7)Li} that give us details on PYR14(+)/X(-) and PYR14(+)/Li(+) contacts. We confirm the presence of [Li(X)2](-) coordinated species in all systems. The long-range, intermolecular NOEs have been detected and provide information on the ions' organization beyond the first solvation sphere. The ionic conductivity, viscosity and self-diffusion coefficients of the ionic mixtures have also been measured. The activation energies for the diffusion of the individual ions and for the fluidity are compared with those for the pure ILs. Finally, density functional calculations on [Li(BETI)2](-), [Li(IM14)2](-), and [Li(TFSI)2](-) complexes demonstrate that the minimum energy structures for all systems correspond to a tetrahedral coordination of the Li-ion by four oxygen atoms of the anions. Assuming very simple key steps for the Li(+) diffusion process (i.e., the concerted breaking and formation of Li-O bonds or the rearrangement around a tetrahedrally coordinated Li(+)), we calculate activation barriers that agree well with the experimental results (approximately 46 kJ/mol, in all systems).

A solid state density functional study of crystalline thiophene-based oligomers and polymers.

We present the results of a molecular modeling study of several thiophene-based oligomers and polymers by solid state density functional theory (DFT) calculations. In particular, we consider two polymers for which limit-ordered crystal structures have been reported by our group, on the basis of powder X-ray data analysis: poly(3-(S)-2-methylbutylthiophene) (P3MBT) and forms I' and II of poly(3-butylthiophene) (P3BT). The calculations employing the functional by Perdew and Wang (PWC) in conjunction with the double-ζ polarized numerical basis set (DNP) demonstrate that a standard quantum mechanical (QM) approach for solid phases can provide a balanced description of the overall structure and energetics of thiophene-based oligomers and polymers maintaining a moderate computational cost. In addition, the results compare well with those provided by specific force field parametrization developed by our group. In many cases, PWC/DNP models show even closer agreement with experimental crystal structures, making it the method of choice for computationally accessible problems. Finally, solid state DFT minimizations confirm that the reported crystal structures of P3MBT and P3BT correspond to well-defined energy minima.

Molecular modeling of crystalline alkylthiophene oligomers and polymers.

We present the results of a thorough molecular modeling study of several alkylthiophene-based oligomers and polymers. In particular, we consider two polymers whose limit-ordered crystal structures have been recently reported by our group, on the basis of powder X-ray data analysis: poly(3-(S)-2-methylbutylthiophene) (P3MBT) and form I' of poly(3-butylthiophene) (P3BT). We first describe the development of a series general purpose force fields for the simulation of these and related systems. The force fields incorporate the results of ab initio calculations of the bond torsion energies of selected oligomers and differ in the set of atomic charges used to represent the electrostatic interactions. We then present the results of an extensive validation of these force fields, by means of molecular mechanics (MM) energy minimizations and molecular dynamics (MD) simulations of the crystal structures of these oligomers and polymers. While our "best" force field does not outperform the others on each of the investigated systems, it provides a balanced description of their overall structure and energetics. Finally, our MM minimizations and MD simulations confirm that the reported crystal structures of P3MBT and P3BT are stable and correspond to well-defined energetic minima. The room-temperature MD simulations reveal a certain degree of side-chain disorder, even in our virtually defect-free polymer crystal models.

Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides.

Partially modified retro- (PMR) and retro-inverso (PMRI) psi[NHCH(CF(3))]Gly peptides, a conceptually new class of peptidomimetics, have been synthesized in wide structural diversity and variable length by aza-Michael reaction of enantiomerically pure alpha-amino esters and peptides with enantiomerically and geometrically pure N-4,4,4-trifluorocrotonoyl-oxazolidin-2-ones. The factors underlying the observed moderate to good diastereocontrol have been investigated. The conformations of model PMR-psi[NHCH(CF(3))]Gly tripeptides have been studied in solution by (1)H NMR spectroscopy supported by MD calculations, as well as in the solid-state by X-ray diffraction. Remarkable stability of turn-like conformations, comparable to that of parent malonyl-based retropeptides, was evidenced, as a likely consequence of two main factors: 1) severe torsional restrictions about sp(3) bonds in the [CO-CH(2)-CH(CF(3))-NH-CH(R)-CO] module, which is biased by the stereoelectronically demanding CF(3) group and the R side chain; 2) formation of nine-membered intramolecularly hydrogen-bonded rings, which have been clearly detected both in CHCl(3) solution and in some crystal structures. The former factor seems to be more important, as turn-like conformations were found in the solid-state even in the absence of intramolecular hydrogen bonding. The relative configuration of the -C*H(CF(3))NHC*H(R)- stereogenic centers has a major effect on the stability of the turn-like conformation, which seems to require a syn stereochemistry. X-ray diffraction and ab initio computational studies showed that the [-CH(CF(3))NH-] group can be seen as a sort of hybrid between a peptide bond mimic and a proteolytic transition state analogue, as it combines some of the properties of a peptidyl -CONH- group (low NH basicity, CH(CF(3))-NH-CH backbone angle close to 120 degrees, C-CF(3) bond substantially isopolar with the C=O) with some others of the tetrahedral intermediate [-C(OX)(O(-))NH-] involved in the protease-mediated hydrolysis reaction of a peptide bond (high electron density on the CF(3) group, tetrahedral backbone carbon).